Membraneless microfluidic fuel cells (MFCs) have garnered tremendous interest as micropower devices, which exploit the colaminar nature of two aqueous electrolytes to separate the anode and cathode and avoid the membrane usually used in a fuel cell. Our previous research shows that the performance of FeCl₃-based MFCs with catalyst-free cathodes is mainly limited by the cathode. To improve the power output of these MFCs, we activated the carbon paper cathode by an electrochemical method in the three solutions (Na₂SO₄, NaOH, and H₂SO₄) to improve the electrochemical characteristics of the carbon paper cathode. The surface functionalities and defects, reduction activation of iron ions as the oxidant, cathode resistance, and performance of FeCl₃-based MFCs were measured and compared. Our work shows that the electrochemical activation of the carbon paper in different solutions is a simple and effective method to enhance the electrochemical characteristics of the carbon paper cathode and improve the performance of the FeCl₃-based MFC. Also, the MFC with the carbon paper cathode activated in the H₂SO₄ solution reaches the optimum performance: 235.6 mW cm^-3 in volumetric power density and 1063.33 mA cm^-3 in volumetric limiting current density, which are 1.58 and 1.52 times as much as that of a MFC with an untreated carbon paper cathode, respectively. This best performance can be attributed to the cathode activated in the H₂SO₄ solution with the largest number of oxygen-containing functional groups, the largest electrochemical active surface area, strongest reduction of iron ions, and least resistance of the cathode.